BCAP31 c.477+16C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0229%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +16 | near-intronic (+16 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.1 | GERP -2.8 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 0.295 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0229%
Middle Eastern · 1/4,362 alleles
Filtering AF
0.00339%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00215%
Overall
0.00149%
18/1,207,288 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0229% | 4,362 |
| African / African-American | 0.00875% | 11,429 |
| Finnishnot grpmax-eligible | 0.00431% | 23,177 |
| Remaining individualsnot grpmax-eligible | 0.00422% | 23,711 |
| European (non-Finnish) | 0.000895% | 111,671 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BCAP31
- Coding
- c.477+16C>T
- MANE Select
- NM_001256447
- dbSNP
- rs782131581
- Type
- single nucleotide variant
- Location
- chrX:153703943 (GRCh38)
- Structure
- AlphaFold pLDDT 84.74 · 3 PDB
Similar variants
- BCAP31 p.Arg118Cys Uncertain significance ★★ ⚠ same type
- BCAP31 p.Glu245Lys Uncertain significance ★★ ⚠ same type
- BCAP31 p.Gly165Arg Uncertain significance ★★ ⚠ same type
- BCAP31 p.Gly239Asp Uncertain significance ★★ ⚠ same type
- BCAP31 p.Ile56Val Uncertain significance ★★ ⚠ same type
- BCAP31 p.Leu226Val Uncertain significance ★★ ⚠ same type
- BCAP31 p.Leu40Pro Uncertain significance ★★ ⚠ same type
- BCAP31 p.Lys30Arg Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bcap31-c-477-plus-16c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown